Hi M, thanks for the compliments on our site, glad you are finding it useful!
You have several options like you said for the leg to Drake Bay, but the best way to save time getting back to San Jose (5-6 hrs from Sierpe) is to fly. If you are following the Two Week Itinerary, you could drop the car off in Manuel Antonio and then take a shuttle to Sierpe to meet the boat. There are a couple of rental companies that allow drop-off in Sierpe but it usually works out to be less expensive if you use our Rental Car Discount through Adobe and drop it off in Manuel Antonio/Quepos (they don’t have an office in Sierpe). If you would rather keep the car the whole time and park at Sierpe, that is possible too. Read our post: Drake Bay: Costa Rica Unplugged, which has parking and boat shuttle information. Have a fantastic trip!